Bioinformatic and Molecular Analysis of Satellite Repeat Diversity in Genomes.

Bioinformatic and molecular characterization of satellite repeats was performed to understand the impact of their diversification on genome evolution. Satellite repeat diversity was evaluated in four cultivated and wild species, including the diploid species and , as well as the tetraploid species and . We comparatively characterized six satellite repeat families using in total 76 clones with 180 monomers. We observed that the monomer units of VaccSat1, VaccSat2, VaccSat5, and VaccSat6 showed a higher order repeat (HOR) structure, likely originating from the organization of two adjacent subunits with differing similarity, length and size. Moreover, VaccSat1, VaccSat3, VaccSat6, and VaccSat7 were found to have sequence similarity to parts of transposable elements. We detected satellite-typical tandem organization for VaccSat1 and VaccSat2 in long arrays, while VaccSat5 and VaccSat6 distributed in multiple sites over all chromosomes of tetraploid , presumably in long arrays. In contrast, very short arrays of VaccSat3 and VaccSat7 are dispersedly distributed over all chromosomes in the same species, likely as internal parts of transposable elements. We provide a comprehensive overview on satellite species specificity in , which are potentially useful as molecular markers to address the taxonomic complexity of the genus, and provide information for genome studies of this genus.